North Ayrshire Council staff have moved to recover the money for local tenants following an announcement by the Department for Work and Pensions (DWP) last month.
The DWP announced that residents should not have been penalised under the spare room subsidy legislation - commonly known as the "bedroom tax".
Investigations by Council staff showed that 204 North Ayrshire households had been affected by a loophole around continuous Housing Benefit claims.
A total of £99,336 in housing benefit has been reimbursed to 176 council tenants and 28 housing association tenants.
Tenants can apply for financial support through the council's Discretionary Housing Payment Fund.